1DWL

The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM 

wwPDB Validation

Currently 1DWL does not have a wwPDB validation report.


This is version 1.2 of the entry. See complete history

Literature

Heteronuclear NMR and Soft Docking: An Experimental Approach for a Structural Model of the Cytochrome C553-Ferredoxin Complex

Morelli, X.Dolla, A.Czjzek, M.Palma, P.N.Blasco, F.Krippahl, L.Moura, J.J.G.Guerlesquin, F.

(2000) Biochemistry 39: 2530

  • Also Cited By: 1E08

  • PubMed Abstract: 
  • The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints ...

    The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c553-ferredoxin complex is used as a model of numerous electron-transfer complexes. The 15N-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. 1H and 15N chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 A2) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.


    Related Citations: 
    • Bigger: A New (Soft) Docking Algorithm for Predicting Protein Interactions
      Palma, P.N.,Krippahl, L.,Wampler, J.E.,Moura, J.J.G.
      (2000) Proteins: Struct.,Funct., Genet. 39: 372
    • Mapping the Cytochrome C553 Interacting Site Using 1H and 15N NMR
      Morelli, X.,Guerlesquin, F.
      (1999) FEBS Lett. 460: 77


    Organizational Affiliation

    Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN I
A
59Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310)N/A
Find proteins for P07485 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Go to UniProtKB:  P07485
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C553
B
79Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)Gene Names: cyf
Find proteins for P04032 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P04032
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM 
  • Olderado: 1DWL Olderado

Structure Validation

Currently 1DWL does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-10
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance